Search found 346 matches

by SaxsMax
2008.03.25 21:12
Forum: Working with Models
Topic: question for CRYSOL 2.5
Replies: 2
Views: 4200

Dro of 0.075 e/A3 is indeed a bit too much and kept for special cases. Normally, it should not exceed 0.05. On the other hand, please notice that for small proteins (like lysozyme) the contribution of the shell is more significant compared to larger particles as atomic and excluded volume scattering...
by SaxsMax
2008.03.25 20:58
Forum: Working with Models
Topic: CRYSOL paper: About Correct formulas for (12) and (13)
Replies: 1
Views: 3834

"Correction 1" is correct as d=s/2PI
by SaxsMax
2008.03.20 21:26
Forum: Ab Initio Shape Determination
Topic: Gasbor and double helix
Replies: 2
Views: 3544

Unfortunately there is no helical symmetry in Gasbor.
by SaxsMax
2008.03.20 21:24
Forum: Ab Initio Shape Determination
Topic: Program for make many run automatically with gasbor
Replies: 3
Views: 4040

As gasbor can be done in a batch mode
(for help type e.g. "gasbor22i.exe /h")
you can simply create a bat file containing
multiple Gasbor calls
by SaxsMax
2008.03.20 21:15
Forum: Working with Models
Topic: Option for explicit hydrogens (CRYSOL)
Replies: 1
Views: 4197

Normally, all hydrogens are ignored by Crysol while reading PDB file and then simulated according to the atomic group. "Account for explicit hydrogens" option gives the possibility to read all hydrogens from the PDB file. In this case Crysol will not add any further hydrogens and all the atoms are h...
by SaxsMax
2008.03.20 21:09
Forum: Working with Models
Topic: Ra and Vol after parameter fitting (CRYSOL logfile)
Replies: 3
Views: 5349

Hydra is hydration which is computes as following

Mh2o (Border volume)*(Solvent density+Border contrast)
---- * -----------------------------------------------
Eh2o Molecular mass of the macromolecule

where Mh2o = 18 dalton, Eh2o = 10 electrons
by SaxsMax
2008.03.20 21:05
Forum: Working with Models
Topic: Ra and Vol after parameter fitting (CRYSOL logfile)
Replies: 3
Views: 5349

Indeed, by the prediction of the scattering without fitting the data (i.e. with the default parameters) V=N*4/3*PI*ra^3 However in case of fitting the experimental data the ra and volume parameters are decoupled and the above equation is not kept in the adjustment of ra and vol minimizing the discre...
by SaxsMax
2008.03.06 14:13
Forum: Rigid Body Modelling
Topic: what is the principle in transformation subunit of MASSHA?
Replies: 1
Views: 3377

Massha does the local refinement of the models,
so that it is better to have a rough idea how the subunits are
arranged. If you need to do a global search it is better to use SASREF instead.

Ideally, chi should be close to 1.0
by SaxsMax
2008.03.06 14:08
Forum: Ab Initio Shape Determination
Topic: Gasbor22iqw and Gasbor22pqw
Replies: 1
Views: 2973

i stands for intensity, i.e. this is the reciprocal space version fitting the
experimental scattering data.
p stand for p(r), i.e. this is a real space version which fits distance distribution function computed from the SAXS curve
by SaxsMax
2008.03.06 14:06
Forum: Ab Initio Shape Determination
Topic: DAMMIN GASBOR AND RNA molecules
Replies: 1
Views: 3153

Probably nothing has to be adjusted in DAMMIN.
On contrary, GASBOR is only applicable for proteins
and it is better to avoid using it for nucleic acids.
by SaxsMax
2008.03.06 14:04
Forum: Ab Initio Shape Determination
Topic: Gasbor and high NSD values
Replies: 2
Views: 4482

In general, it is normal that GASBOR models
yield higher NSD values compared to DAMMIN ones.
However, NSD of 2.8- 3.2 is a bit too much. Do the superposed
GASBOR models look the same by eye?
by SaxsMax
2008.02.25 20:59
Forum: Working with Models
Topic: shell size
Replies: 1
Views: 3694

The shell width is indeed a fixed parameter in Crysol, however in most of applications only the product of the shell width and the shell contrast matters. So, one could try to vary the density of the shell instead of changing its width. Also the use of tentative detergent molecules around the protei...
by SaxsMax
2008.02.13 22:09
Forum: Ab Initio Shape Determination
Topic: MONSA - control and master files
Replies: 1
Views: 3320

The first phase is the part of the protein corresponding to the fragment dat. Then the second phase is the rest. The volumes in MASTER file were evaluated using Primus (Porod Button) and DAMMIN. I put the volume and RG from the fragment and the protein. This should be the volumes of the two parts an...
by SaxsMax
2008.02.13 21:53
Forum: Rigid Body Modelling
Topic: Defining starting configuration SASREF
Replies: 1
Views: 3291

Yes, and this is even the default option,
i.e. if you do not shift and rotate the subunits on purpose.
by SaxsMax
2008.01.25 13:56
Forum: Ab Initio Shape Determination
Topic: DAMMIN/MONSA for natively or partially unfolded protein
Replies: 1
Views: 3582

EOM package seems to be the most suitable for the case